6VC8 | pdb_00006vc8

Crystal structure of wild-type KRAS4b(1-169) in complex with GMPPNP and Mg ion

• PDB DOI: https://doi.org/10.2210/pdb6VC8/pdb

• Classification: ONCOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-20 Released: 2021-02-10 
• Deposition Author(s): Tran, T.H., Davies, D.R., Edwards, T.E., Simanshu, D.K.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.277 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins.

Ingolfsson, H.I., Neale, C., Carpenter, T.S., Shrestha, R., Lopez, C.A., Tran, T.H., Oppelstrup, T., Bhatia, H., Stanton, L.G., Zhang, X., Sundram, S., Di Natale, F., Agarwal, A., Dharuman, G., Kokkila Schumacher, S.I.L., Turbyville, T., Gulten, G., Van, Q.N., Goswami, D., Jean-Francois, F., Agamasu, C., Hettige, J.J., Travers, T., Sarkar, S., Surh, M.P., Yang, Y., Moody, A., Liu, S., Van Essen, B.C., Voter, A.F., Ramanathan, A., Hengartner, N.W., Simanshu, D.K., Stephen, A.G., Bremer, P.T., Gnanakaran, S., Glosli, J.N., Lightstone, F.C., McCormick, F., Nissley, D.V., Streitz, F.H.

(2022) Proc Natl Acad Sci U S A 119

• PubMed: 34983849 
• DOI: https://doi.org/10.1073/pnas.2113297119
• Primary Citation Related Structures: 
  6VC8


• PubMed Abstract: 
  

  RAS is a signaling protein associated with the cell membrane that is mutated in up to 30% of human cancers. RAS signaling has been proposed to be regulated by dynamic heterogeneity of the cell membrane. Investigating such a mechanism requires near-atomistic detail at macroscopic temporal and spatial scales, which is not possible with conventional computational or experimental techniques. We demonstrate here a multiscale simulation infrastructure that uses machine learning to create a scale-bridging ensemble of over 100,000 simulations of active wild-type KRAS on a complex, asymmetric membrane. Initialized and validated with experimental data (including a new structure of active wild-type KRAS), these simulations represent a substantial advance in the ability to characterize RAS-membrane biology. We report distinctive patterns of local lipid composition that correlate with interfacially promiscuous RAS multimerization. These lipid fingerprints are coupled to RAS dynamics, predicted to influence effector binding, and therefore may be a mechanism for regulating cell signaling cascades.

---

Organizational Affiliation: 
• Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550.
Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545.
RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701.
Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550.
Department of Mathematics and Statistics, San José State University, San José, CA 95192.
Data Centric Systems, IBM T. J. Watson Research Center, Yorktown Heights, NY 10598.
Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545.
Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545.
Computing, Environment & Life Sciences Directorate, Argonne National Laboratory, Lemont, IL 60439.
RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701; [e-mail] [e-mail] [e-mail].
Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94115.
Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550; [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 59.63 kDa 
• Atom Count: 3,689 
• Modeled Residue Count: 470 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	A, B, C	170	Homo sapiens	Mutation(s): 0  Gene Names: KRAS, KRAS2, RASK2 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens) Explore P01116  Go to UniProtKB:  P01116
PHAROS:  P01116 GTEx:  ENSG00000133703

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP (Subject of Investigation/LOI)	D [auth A], F [auth B], H [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.277 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.21	α = 90
b = 82.33	β = 112.92
c = 88.14	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Tran, T.H., Davies, D.R., Edwards, T.E., Simanshu, D.K.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2021-02-10
  Type: Initial release
  
• Version 1.1: 2022-01-12
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Refinement description